Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women - PubMed (original) (raw)

. 2016 Jan;144(1):123-37.

doi: 10.1017/S0950268815000965. Epub 2015 Jun 11.

B Ma 2, A O Famooto 1, S N Adebamowo 1, R A Offiong 3, O Olaniyan 4, P S Dakum 1, C M Wheeler 5, D Fadrosh 2, H Yang 2, P Gajer 2, R M Brotman 2, J Ravel 2, C A Adebamowo 6

Affiliations

Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women

E O Dareng et al. Epidemiol Infect. 2016 Jan.

Abstract

In this study, we evaluated the association between high-risk human papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in Nigeria between April and August 2012. Vaginal bacterial composition was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV genotyping test. We used exact logistic regression models to evaluate the association between community state types (CSTs) of vaginal microbiota and hrHPV infection, weighted UniFrac distances to compare the vaginal microbiota of individuals with prevalent hrHPV to those without prevalent hrHPV infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants; CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in 7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection and a decreased abundance of Lactobacillus sp. with increased abundance of anaerobes particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P < 0·05). These results are hypothesis generating and further studies are required.

Keywords: HIV/AIDS; human papilloma virus (HPV); public health.

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Conflict of interest statement

None.

Figures

Fig. 1.

Fig. 1.

Heat map of relative abundance for the 50 most abundant bacterial taxa found in the vaginal bacterial communities of all participants in the study. Ward linkage clustering was used to cluster samples based on their Jensen–Shannon distance calculated in the

vegan

package in R [44]. Identified community state types (CSTs) are labelled as I, III, and IV, according to the previous naming convention [51]. hrHPV, High-risk human papillomavirus.

Fig. 2.

Fig. 2.

Weighted UniFrac principal coordinates analysis (PCoA) plot comparing sample distribution belonging to different community state types (CSTs). See Figure 1 for sample CST assignments used in this figure.

Fig. 3.

Fig. 3.

Histogram of weighted UniFrac distance between samples by human papillomavirus (HPV)/HIV metadata. The distribution of distance between samples of HPV + /HIV–, HPV–/HIV–, HPV + /HIV + , and HPV–/HIV+ women is shown.

Fig. 4.

Fig. 4.

(a) Cladogram representing the taxonomic hierarchical structure of the identified phylotype biomarkers, generated using LEfSe [47]. Phylotype biomarkers are identified comparing samples collected from HIV–/HPV– and HIV–/HPV+ participants. Each filled circle represents one biomarker. Red, phylotypes statistically overrepresented under the condition of HPV + /HIV–; green, phylotypes overrepresented under the condition of HPV–/HIV–; yellow, phylotypes for which relative abundance is not significantly different between the two conditions. The diameter of each circle is proportional to the phylotype's effect size, phylum and class are indicated in their names on the cladogram and the order, family, or genera are given in the key. (b) Identified phylotype biomarkers ranked by effect size in HIV– women. The phylotype biomarkers are identified as being significantly abundant comparing samples collected from HPV– and HPV+ women with an alpha value <0·05. The graph was generated using the LEfSe program. The phylotypes are ranked according to their effect size that are associated with different conditions with the highest median. The Linear Discriminant Analysis (LDA) score [47] at the log10 scale is indicated at the bottom. The greater the LDA score is, the more significant the phylotype biomarker is in the comparison.

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